So I think I know the issue, but I don't know how to correct it. The truck keeps throwing a code about the non-volatile RAM (NVRAM) that won't clear. I think what has happened is the programming "thinks" it's fine, and it is fine enough to start the engine, run like garbage, and throw a bunch of codes. THe SCT Tuner and the IDS system cannot not convince it to erase and re-write the programming. Each time I try to re-write the programming is does it quickly, says it was sent and everything is good to go. It makes me think it's doing a check and the check is saying everything is good to go.
Similar issue with the calibration ( I assume these are separate). In one instance I was able to get it to try to really set the calibration. In doing so it shut down the entire system. I believe this to be because the programming is incorrect and thus the PCM can't accept the calibration.
If I could find a way to truly ERASE the PCM and make it think it's blank as blank could be THEN program it, I think I could save buying another PCM.
@Tirefryr, I'm going to see if FordTechMakuloco will be willing to shed light on the situation.